Showing papers by "Manuel Delgado-Baquerizo published in 2018"

A global atlas of the dominant bacteria found in soil

Abstract: The immense diversity of soil bacterial communities has stymied efforts to characterize individual taxa and document their global distributions. We analyzed soils from 237 locations across six continents and found that only 2% of bacterial phylotypes (~500 phylotypes) consistently accounted for almost half of the soil bacterial communities worldwide. Despite the overwhelming diversity of bacterial communities, relatively few bacterial taxa are abundant in soils globally. We clustered these dominant taxa into ecological groups to build the first global atlas of soil bacterial taxa. Our study narrows down the immense number of bacterial taxa to a “most wanted” list that will be fruitful targets for genomic and cultivation-based efforts aimed at improving our understanding of soil microbes and their contributions to ecosystem functioning.

Drought consistently alters the composition of soil fungal and bacterial communities in grasslands from two continents.

Abstract: The effects of short-term drought on soil microbial communities remain largely unexplored, particularly at large scales and under field conditions. We used seven experimental sites from two continents (North America and Australia) to evaluate the impacts of imposed extreme drought on the abundance, community composition, richness, and function of soil bacterial and fungal communities. The sites encompassed different grassland ecosystems spanning a wide range of climatic and soil properties. Drought significantly altered the community composition of soil bacteria and, to a lesser extent, fungi in grasslands from two continents. The magnitude of the fungal community change was directly proportional to the precipitation gradient. This greater fungal sensitivity to drought at more mesic sites contrasts with the generally observed pattern of greater drought sensitivity of plant communities in more arid grasslands, suggesting that plant and microbial communities may respond differently along precipitation gradients. Actinobateria, and Chloroflexi, bacterial phyla typically dominant in dry environments, increased their relative abundance in response to drought, whereas Glomeromycetes, a fungal class regarded as widely symbiotic, decreased in relative abundance. The response of Chlamydiae and Tenericutes, two phyla of mostly pathogenic species, decreased and increased along the precipitation gradient, respectively. Soil enzyme activity consistently increased under drought, a response that was attributed to drought-induced changes in microbial community structure rather than to changes in abundance and diversity. Our results provide evidence that drought has a widespread effect on the assembly of microbial communities, one of the major drivers of soil function in terrestrial ecosystems. Such responses may have important implications for the provision of key ecosystem services, including nutrient cycling, and may result in the weakening of plant-microbial interactions and a greater incidence of certain soil-borne diseases.

New insights into the role of microbial community composition in driving soil respiration rates

Abstract: Microbial community plays critical roles in driving soil carbon (C) cycling in terrestrial ecosystems. However, we lack empirical evidence to demonstrate the role of microbial community in driving soil respiration - a key ecosystem process for global sustainability and climate regulation. Here, we used a long-term field experiment including multiple management practices, to identify, via statistical modeling, the role of microbial community composition in influencing soil respiration. We analyzed major soil properties and microbial (both bacterial and fungal) abundance, diversity and community composition. We found that different management regimes led to different soil respiration rates. Most importantly, microbial community composition explained a unique portion of the variation in soil respiration, which cannot be accounted for by key respiration drivers such as soil properties and other microbial attributes (richness and total abundance). Microbial biomass and fungal richness were also identified as key drivers of soil respiration. Our results indicate that inclusions of microbial compositional data in Earth system models can be potentially used to improve our capacity to predict changes in soil C balance under changing environments.

Ecological drivers of soil microbial diversity and soil biological networks in the Southern Hemisphere.

Abstract: The ecological drivers of soil biodiversity in the Southern Hemisphere remain underexplored. Here, in a continental survey comprising 647 sites, across 58 degrees of latitude between tropical Australia and Antarctica, we evaluated the major ecological patterns in soil biodiversity and relative abundance of ecological clusters within a co-occurrence network of soil bacteria, archaea and eukaryotes. Six major ecological clusters (modules) of co-occurring soil taxa were identified. These clusters exhibited strong shifts in their relative abundances with increasing distance from the equator. Temperature was the major environmental driver of the relative abundance of ecological clusters when Australia and Antarctica are analyzed together. Temperature, aridity, soil properties and vegetation types were the major drivers of the relative abundance of different ecological clusters within Australia. Our data supports significant reductions in the diversity of bacteria, archaea and eukaryotes in Antarctica vs. Australia linked to strong reductions in temperature. However, we only detected small latitudinal variations in soil biodiversity within Australia. Different environmental drivers regulate the diversity of soil archaea (temperature and soil carbon), bacteria (aridity, vegetation attributes and pH) and eukaryotes (vegetation type and soil carbon) across Australia. Together, our findings provide new insights into the mechanisms driving soil biodiversity in the Southern Hemisphere.

Detecting macroecological patterns in bacterial communities across independent studies of global soils.

Abstract: The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries. Whereas previous meta-analysis efforts have focused on bacterial diversity measures or abundances of major taxa, we show that disparate amplicon sequence data can be combined at the taxonomy-based level to assess bacterial community structure. We find that rarer taxa are more important for structuring soil communities than abundant taxa, and that these rarer taxa are better predictors of community structure than environmental factors, which are often confounded across studies. We conclude that combining data from independent studies can be used to explore bacterial community dynamics, identify potential ‘indicator’ taxa with an important role in structuring communities, and propose hypotheses on the factors that shape bacterial biogeography that have been overlooked in the past.

Soil fungal abundance and plant functional traits drive fertile island formation in global drylands

Abstract: Dryland vegetation is characterized by discrete plant patches that accumulate and capture soil resources under their canopies. These “fertile islands” are major drivers of dryland ecosystem structure and functioning, yet we lack an integrated understanding of the factors controlling their magnitude and variability at the global scale. We conducted a standardized field survey across 236 drylands from five continents. At each site, we measured the composition, diversity and cover of perennial plants. Fertile island effects were estimated at each site by comparing composite soil samples obtained under the canopy of the dominant plants and in open areas devoid of perennial vegetation. For each sample, we measured 15 soil variables (functions) associated with carbon, nitrogen and phosphorus cycling and used the relative interaction index to quantify the magnitude of the fertile island effect for each function. In 80 sites, we also measured fungal and bacterial abundance (quantitative PCR) and diversity (Illumina MiSeq). The most fertile islands, i.e. those where a higher number of functions were simultaneously enhanced, were found at lower elevation sites with greater soil pH values and sand content under semiarid climates, particularly at locations where the presence of tall woody species with a low-specific leaf area increased fungal abundance beneath plant canopies, the main direct biotic controller of the fertile island effect in the drylands studied. Positive effects of fungal abundance were particularly associated with greater nutrient contents and microbial activity (soil extracellular enzymes) under plant canopies. Synthesis. Our results show that the formation of fertile islands in global drylands largely depends on: (1) local climatic, topographic and edaphic characteristics, (2) the structure and traits of local plant communities and (3) soil microbial communities. Our study also has broad implications for the management and restoration of dryland ecosystems worldwide, where woody plants are commonly used as nurse plants to enhance the establishment and survival of beneficiary species. Finally, our results suggest that forecasted increases in aridity may enhance the formation of fertile islands in drylands worldwide.

Consistent responses of soil microbial taxonomic and functional attributes to mercury pollution across China

Abstract: The ecological consequences of mercury (Hg) pollution—one of the major pollutants worldwide—on microbial taxonomic and functional attributes remain poorly understood and largely unexplored. Using soils from two typical Hg-impacted regions across China, here, we evaluated the role of Hg pollution in regulating bacterial abundance, diversity, and co-occurrence network. We also investigated the associations between Hg contents and the relative abundance of microbial functional genes by analyzing the soil metagenomes from a subset of those sites. We found that soil Hg largely influenced the taxonomic and functional attributes of microbial communities in the two studied regions. In general, Hg pollution was negatively related to bacterial abundance, but positively related to the diversity of bacteria in two separate regions. We also found some consistent associations between soil Hg contents and the community composition of bacteria. For example, soil total Hg content was positively related to the relative abundance of Firmicutes and Bacteroidetes in both paddy and upland soils. In contrast, the methylmercury (MeHg) concentration was negatively correlated to the relative abundance of Nitrospirae in the two types of soils. Increases in soil Hg pollution correlated with drastic changes in the relative abundance of ecological clusters within the co-occurrence network of bacterial communities for the two regions. Using metagenomic data, we were also able to detect the effect of Hg pollution on multiple functional genes relevant to key soil processes such as element cycles and Hg transformations (e.g., methylation and reduction). Together, our study provides solid evidence that Hg pollution has predictable and significant effects on multiple taxonomic and functional attributes including bacterial abundance, diversity, and the relative abundance of ecological clusters and functional genes. Our results suggest an increase in soil Hg pollution linked to human activities will lead to predictable shifts in the taxonomic and functional attributes in the Hg-impacted areas, with potential implications for sustainable management of agricultural ecosystems and elsewhere.

Plant attributes explain the distribution of soil microbial communities in two contrasting regions of the globe.

Abstract: We lack strong empirical evidence for links between plant attributes (plant community attributes and functional traits) and the distribution of soil microbial communities at large spatial scales. Using datasets from two contrasting regions and ecosystem types in Australia and England, we report that aboveground plant community attributes, such as diversity (species richness) and cover, and functional traits can predict a unique portion of the variation in the diversity (number of phylotypes) and community composition of soil bacteria and fungi that cannot be explained by soil abiotic properties and climate. We further identify the relative importance and evaluate the potential direct and indirect effects of climate, soil properties and plant attributes in regulating the diversity and community composition of soil microbial communities. Finally, we deliver a list of examples of common taxa from Australia and England that are strongly related to specific plant traits, such as specific leaf area index, leaf nitrogen and nitrogen fixation. Together, our work provides new evidence that plant attributes, especially plant functional traits, can predict the distribution of soil microbial communities at the regional scale and across two hemispheres.

Global gaps in soil biodiversity data.

Abstract: To the Editor — Soil biodiversity represents a major terrestrial biodiversity pool, supports key ecosystem services and is under pressure from human activities1. Yet soil biodiversity has been neglected from many global biodiversity assessments and policies. This omission is undoubtedly related to the paucity of comprehensive information on soil biodiversity, particularly on larger spatial scales. Information on belowground species distributions, population trends, endemism and threats to belowground diversity is important for conservation prioritization, but is practically non-existent. As a consequence, much of our understanding of global macroecological patterns in biodiversity, as well as mapping of global biodiversity hotspots, has been based on aboveground taxa (such as plants2) and has not considered the functionally vital, but less visible, biodiversity found in soil. We mapped the study sites from existing global datasets on soil biodiversity (soil macrofauna3, fungi4 and bacteria5) to examine key data gaps (Fig. 1). Our map indicates significant gaps in soil biodiversity data across northern latitudes, including most of Russia and Canada. Data are also lacking from much of central Asia and central Africa (for example, the Sahara Desert), as well as many tropical regions. The higher density of soil biodiversity sampling sites in Europe and the United States is similar to patterns observed for data on terrestrial bird, mammal and amphibian species6, as well as plants7. Yet, in such aboveground datasets, the gaps in understudied regions are much less pronounced than in the soil biodiversity datasets shown here. The comparative lack of soil biodiversity data across these regions limits our ability to examine global macroecological patterns and to quantify potential mismatches between aboveground and soil biodiversity. The potential for such mismatches (areas with high aboveground diversity, but low soil biodiversity, or vice versa) may be substantial, as evidence suggests that plant species richness declines more rapidly towards the North Pole than fungal species richness, which reaches a plateau4. Soil ecologists are increasingly conducting their own large-scale assessments (such as the African Soil Microbiology Project8) and additional databases on soil biodiversity are beginning to be developed9, in part through the Global Soil Biodiversity Initiative. However, increased efforts to fill these gaps and to compile additional global datasets on other soil taxa (for example, mesofauna) are needed to allow more detailed analyses of soil biodiversity on broad spatial scales. Of major concern is the lack of a global consensus on sampling strategies and methodological approaches to assess soil biodiversity, which in many cases makes it challenging to compare datasets directly. Furthermore, greater cooperation with conservation biologists and policymakers is needed to better integrate soil biodiversity into global policies. For instance, soil biodiversity should be more explicitly considered in the post-2020 global biodiversity framework10 that will follow the Strategic Plan for Biodiversity 2011–2020 and in future assessments of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services11. These evident gaps in soil biodiversity data restrict our ability to develop policies to protect soil biodiversity. We argue that addressing these data gaps will ultimately benefit human well-being1 and provide an impetus for increased policy-relevant research on soil biodiversity. ❐

Cascading effects from plants to soil microorganisms explain how plant species richness and simulated climate change affect soil multifunctionality

Abstract: Despite their importance, how plant communities and soil microorganisms interact to determine the capacity of ecosystems to provide multiple functions simultaneously (multifunctionality) under climate change is poorly known. We conducted a common garden experiment using grassland species to evaluate how plant functional structure and soil microbial (bacteria and protists) diversity and abundance regulate soil multifunctionality responses to joint changes in plant species richness (one, three and six species) and simulated climate change (3°C warming and 35% rainfall reduction). The effects of species richness and climate on soil multifunctionality were indirectly driven via changes in plant functional structure and their relationships with the abundance and diversity of soil bacteria and protists. More specifically, warming selected for the larger and most productive plant species, increasing the average size within communities and leading to reductions in functional plant diversity. These changes increased the total abundance of bacteria that, in turn, increased that of protists, ultimately promoting soil multifunctionality. Our work suggests that cascading effects between plant functional traits and the abundance of multitrophic soil organisms largely regulate the response of soil multifunctionality to simulated climate change, and ultimately provides novel experimental insights into the mechanisms underlying the effects of biodiversity and climate change on ecosystem functioning.

Ecological Analyses of Mycobacteria in Showerhead Biofilms and Their Relevance to Human Health

Abstract: Bacteria within the genus Mycobacterium can be abundant in showerheads, and the inhalation of aerosolized mycobacteria while showering has been implicated as a mode of transmission in nontuberculous mycobacterial (NTM) lung infections. Despite their importance, the diversity, distributions, and environmental predictors of showerhead-associated mycobacteria remain largely unresolved. To address these knowledge gaps, we worked with citizen scientists to collect showerhead biofilm samples and associated water chemistry data from 656 households located across the United States and Europe. Our cultivation-independent analyses revealed that the genus Mycobacterium was consistently the most abundant genus of bacteria detected in residential showerheads, and yet mycobacterial diversity and abundances were highly variable. Mycobacteria were far more abundant, on average, in showerheads receiving municipal water than in those receiving well water and in U.S. households than in European households, patterns that are likely driven by differences in the use of chlorine disinfectants. Moreover, we found that water source, water chemistry, and household location also influenced the prevalence of specific mycobacterial lineages detected in showerheads. We identified geographic regions within the United States where showerheads have particularly high abundances of potentially pathogenic lineages of mycobacteria, and these "hot spots" generally overlapped those regions where NTM lung disease is most prevalent. Together, these results emphasize the public health relevance of mycobacteria in showerhead biofilms. They further demonstrate that mycobacterial distributions in showerhead biofilms are often predictable from household location and water chemistry, knowledge that advances our understanding of NTM transmission dynamics and the development of strategies to reduce exposures to these emerging pathogens.IMPORTANCE Bacteria thrive in showerheads and throughout household water distribution systems. While most of these bacteria are innocuous, some are potential pathogens, including members of the genus Mycobacterium that can cause nontuberculous mycobacterial (NTM) lung infection, an increasing threat to public health. We found that showerheads in households across the United States and Europe often harbor abundant mycobacterial communities that vary in composition depending on geographic location, water chemistry, and water source, with households receiving water treated with chlorine disinfectants having particularly high abundances of certain mycobacteria. The regions in the United States where NTM lung infections are most common were the same regions where pathogenic mycobacteria were most prevalent in showerheads, highlighting the important role of showerheads in the transmission of NTM infections.

Biocrust-forming mosses mitigate the impact of aridity on soil microbial communities in drylands: observational evidence from three continents.

Abstract: Recent research indicates that increased aridity linked to climate change will reduce the diversity of soil microbial communities and shift their community composition in drylands, Earth's largest biome. However, we lack both a theoretical framework and solid empirical evidence of how important biotic components from drylands, such as biocrust-forming mosses, will regulate the responses of microbial communities to expected increases in aridity with climate change. Here we report results from a cross-continental (North America, Europe and Australia) survey of 39 locations from arid to humid ecosystems, where we evaluated how biocrust-forming mosses regulate the relationship between aridity and the community composition and diversity of soil bacteria and fungi in dryland ecosystems. Increasing aridity was negatively related to the richness of fungi, and either positively or negatively related to the relative abundance of selected microbial phyla, when biocrust-forming mosses were absent. Conversely, we found an overall lack of relationship between aridity and the relative abundance and richness of microbial communities under biocrust-forming mosses. Our results suggest that biocrust-forming mosses mitigate the impact of aridity on the community composition of globally distributed microbial taxa, and the diversity of fungi. They emphasize the importance of maintaining biocrusts as a sanctuary for soil microbes in drylands.

Temperature and aridity regulate spatial variability of soil multifunctionality in drylands across the globe

Abstract: The relationship between the spatial variability of soil multifunctionality (i.e. the capacity of soils to conduct multiple functions; SVM) and major climatic drivers, such as temperature and aridity, has never been assessed globally in terrestrial ecosystems. We surveyed 236 dryland ecosystems from six continents to evaluate the relative importance of aridity and mean annual temperature, and of other abiotic (e.g., texture) and biotic (e.g., plant cover) variables as drivers of SVM, calculated as the averaged coefficient of variation for multiple soil variables linked to nutrient stocks and cycling. We found that increases in temperature and aridity were globally correlated to increases in SVM. Some of these climatic effects on SVM were direct, but others were indirectly driven through reductions in the number of vegetation patches and increases in soil sand content. The predictive capacity of our structural equation modelling was clearly higher for the spatial variability of N- than for C- and P- related soil variables. In the case of N cycling, the effects of temperature and aridity were both direct and indirect via changes in soil properties. For C and P, the effect of climate was mainly indirect via changes in plant attributes. These results suggest that future changes in climate may decouple the spatial availability of these elements for plants and microbes in dryland soils. Our findings significantly advance our understanding of the patterns and mechanisms driving SVM in drylands across the globe, which is critical for predicting changes in ecosystem functioning in response to climate change.

Intransitive competition is common across five major taxonomic groups and is driven by productivity, competitive rank and functional traits

Abstract: TRY is currently supported by DIVERSITAS/Future Earth and the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig. S.S. was supported by the Spanish Government under a Ramon y Cajal contract (RYC-2016-20604). A.L. and M.C.R. acknowledge funding from Deutsche Forschungsgemeinschaft (DFG, grant no: RI 1815/16-1). F.A. has been supported by the Swiss National Science Foundation (grants no. 31003A_135622 and PP00P3_150698). M.D.-B. acknowledges support from the Marie Sklodowska-Curie Actions of the Horizon 2020 Framework Program H2020-MSCA-IF-2016 under REA grant agreement no. 702057. E.A. received financial support from the Swiss National Science Foundation (grant number 31003A_160212). S.B., E.A. and S.S. were partly funded by the DFG Priority Program 1374 “Infrastructure-Biodiversity-Exploratories” (Fi-1246/6-1). Fieldwork permits were issued by the responsible state environmental offices of Baden-Wurttemberg. B.K.S. is supported by Australian Research Council (DP170104634).

Livestock activity increases exotic plant richness, but wildlife increases native richness, with stronger effects under low productivity

Abstract: 1.Grazing by domestic livestock is one of the most widespread land uses worldwide, particularly in rangelands, where it co-occurs with grazing by wild herbivores. Grazing effects on plant diversity are likely to depend on intensity of grazing, herbivore type, coevolution with plants and prevailing environmental conditions. 2.We collected data on climate, plant productivity, soil properties, grazing intensity and herbivore type; and measured their effects on plant species richness from 451 sites across 0.4 M km2 of semi-arid rangelands in eastern Australia. We used structural equation modelling to examine the direct and indirect effects of increasing grazing intensity by different herbivores (cattle, sheep, kangaroos, rabbits) on native and exotic plant species richness across all sites, and in subsets focusing on three woodland communities spanning a gradient in productivity. 3.Direct effects of grazing by all herbivores were strongest under low productivity but waned with increasing productivity. Increases in the intensity of recent and historic livestock grazing corresponded with greater exotic plant richness under low productivity and less native plant richness under both low and moderate productivity. Rabbit effects were greatest under moderate productivity. Overall effects of kangaroos were benign. Grazing indirectly affected native and exotic plant richness by increasing soil phosphorus and reducing soil health (i.e., nutrient cycling). 4.Synthesis and applications. Our study shows that livestock grazing increases exotic species richness but reduces native richness, while kangaroo grazing increases native richness in environments with low productivity. The results provide clear messages for land managers and policy makers: (1) the coexistence of livestock grazing and plant diversity is only possible within more productive environments and (2) grazing under low or moderate productivity will impact upon native and exotic plant richness. This article is protected by copyright. All rights reserved.

Aridity Decouples C:N:P Stoichiometry Across Multiple Trophic Levels in Terrestrial Ecosystems

Abstract: Increases in aridity forecasted by the end of this century will decouple the cycles of soil carbon (C), nitrogen (N) and phosphorus (P) in drylands—the largest terrestrial biome on Earth. Little is known, however, about how changes in aridity simultaneously affect the C:N:P stoichiometry of organisms across multiple trophic levels. It is imperative that we understand how aridity affects ecological stoichiometry so that we can develop strategies to mitigate any effects of changing climates. We characterized the C, N, P concentration and stoichiometry of soils, autotrophs (trees, N-fixing shrubs, grasses and mosses) and heterotrophs (microbes and ants) across a wide aridity gradient in Australia. Our results suggest that increases in aridity by the end of this century may alter the C:N:P stoichiometry of heterotrophs (ants and microbes), non-woody plants and in soil, but will not affect that one from woody plants. In particular, increases in aridity were positively related to C:P and N:P ratios in microbes and ants, negatively related to concentration of C, and the C:N and C:P ratios in mosses and/or short grasses, and not related to the C:N:P stoichiometry of either shrubs or trees. Because of the predominant role of C:N:P stoichiometry in driving nutrient cycling, our findings provide useful contextual information to determine ecological responses in a drier world.

Australian dryland soils are acidic and nutrient‐depleted, and have unique microbial communities compared with other drylands

Abstract: Aim To compare Australian dryland soils with dryland soils globally. Location Australian and global drylands. Methods We used data from standardized surveys of soil properties (C:N:P content and stoichiometry, and pH), and microbes (diversity, composition and correlation networks) from Australian and global drylands, which occupy three-quarters of the Australian land mass and are the largest biome on Earth. Results We found that Australian dryland soils were different, exhibiting characteristics of ancient weathered soils. They had lower pH, total and available P, and total N, and greater C:N and C:P ratios than global dryland soils. Australian soils had distinctive microbial community composition and diversity, with more Proteobacteria and fewer Basidiomycota than global dryland soils, and promoted the abundance of specific microbial phylotypes including pathogens, mycorrhizae and saprobes. Main conclusions Australian dryland soils are clearly different from dryland soils elsewhere. These differences need to be considered when managing dryland soils to avoid unreasonable expectations about plant productivity and carbon stocks, or when predicting likely changes in ecosystem processes resulting from global environmental change.

Pathways regulating decreased soil respiration with warming in a biocrust-dominated dryland.

Abstract: A positive soil carbon (C)-climate feedback is embedded into the climatic models of the IPCC. However, recent global syntheses indicate that the temperature sensitivity of soil respiration (RS ) in drylands, the largest biome on Earth, is actually lower in warmed than in control plots. Consequently, soil C losses with future warming are expected to be low compared with other biomes. Nevertheless, the empirical basis for these global extrapolations is still poor in drylands, due to the low number of field experiments testing the pathways behind the long-term responses of soil respiration (RS ) to warming. Importantly, global drylands are covered with biocrusts (communities formed by bryophytes, lichens, cyanobacteria, fungi, and bacteria), and thus, RS responses to warming may be driven by both autotrophic and heterotrophic pathways. Here, we evaluated the effects of 8-year experimental warming on RS , and the different pathways involved, in a biocrust-dominated dryland in southern Spain. We also assessed the overall impacts on soil organic C (SOC) accumulation over time. Across the years and biocrust cover levels, warming reduced RS by 0.30 μmol CO2 m-2 s-1 (95% CI = -0.24 to 0.84), although the negative warming effects were only significant after 3 years of elevated temperatures in areas with low initial biocrust cover. We found support for different pathways regulating the warming-induced reduction in RS at areas with low (microbial thermal acclimation via reduced soil mass-specific respiration and β-glucosidase enzymatic activity) vs. high (microbial thermal acclimation jointly with a reduction in autotrophic respiration from decreased lichen cover) initial biocrust cover. Our 8-year experimental study shows a reduction in soil respiration with warming and highlights that biocrusts should be explicitly included in modeling efforts aimed to quantify the soil C-climate feedback in drylands.

Livestock grazing and aridity reduce the functional diversity of biocrusts

Abstract: Livestock grazing and climate change are two of the most important global change drivers affecting ecosystem functioning in drylands. Grazing and climate are known to influence the cover and composition of biocrusts, which are substantial components of dryland soils globally. Much less is known, however, about how these global change drivers affect the functional diversity of biocrust communities in these ecosystems. Here, we evaluate the role of increasing aridity and grazing intensity in driving the functional diversity of biocrusts. We collected data on multiple biocrust functional traits and community composition, recent and historic grazing intensity, and vascular plants at 151 sites from drylands in eastern Australia. We then used structural equation modelling and a fourth corner analysis to examine the combined effects of aridity and grazing on biocrust functional diversity and individual functional traits. Aridity had a significant direct suppressive effect on biocrust functional diversity. Effects of grazing by livestock, kangaroos and rabbits on functional diversity were predominantly indirect and suppressive, mediated by a reduction in biocrust cover. Grazing did, however, promote functional diversity via an increase in vascular plant richness, with a concomitant increase in biocrust richness. The overall effect of grazing on biocrust functional diversity however was negative. Fourth corner analyses revealed that livestock grazing had a significant negative effect on the ability of biocrusts to stabilise the soil. Aridity had strong negative effects on biocrust height and their ability to absorb water and capture sediment. Few significant relationships were detected between enzyme-related traits and environmental variables. Our findings provide novel evidence that the combination of increasing aridity and intensified livestock grazing will reduce the functional diversity and capabilities of biocrust communities, with resultant declines in ecosystem functioning.

Functional groups of soil fungi decline under grazing

Abstract: Fungi play vital roles in organic matter decomposition, and mineralisation of phosphorus and nitrogen, are significant plant and animal pathogens, and major mutualistic symbionts with the roots of higher plants. Despite their importance, relatively little is known about the effects of livestock grazing on different functional groups of fungi. We used structural equation modelling to examine how grazing by domestic livestock and native herbivores, and aridity, plant cover and soil carbon influenced four functional groups of soil fungi (ectomycorrhizal fungi, arbuscular mycorrhizal fungi, dung saprobes, plant pathogens) from three microsites (tree, shrub, grass) at 54 woodland sites across 0.4 million km2 of dryland in eastern Australia. Structural equation modelling showed that aridity influenced fungi indirectly by affecting different herbivores and by changing plant cover, which had different effects on different fungal groups. Rabbit grazing had a direct negative effect on ectomycorrhizal and arbuscular mycorrhizal fungi, most likely by disrupting hyphal networks through soil disturbance. Increased cattle grazing was directly positively associated with fungal dung saprobe abundance, and indirectly, negatively associated with dung saprobes by suppressing the positive effects of soil carbon. Sheep had direct and indirect negative effects on the abundance of plant pathogens. Grazing was always an important predictor of the relative abundance of all fungal groups, either directly or indirectly. Thus, overgrazing is likely to have substantial effects on a range of important soil processes controlled by these microorganisms. Overall, our work indicates that increasing grazing, linked to on-going land use intensification to support a growing global population, will have major impacts on fungal functional groups.

Identity of plant, lichen and moss species connects with microbial abundance and soil functioning in maritime Antarctica

Abstract: We lack studies evaluating how the identity of plant, lichen and moss species relates to microbial abundance and soil functioning on Antarctica. If species identity is associated with soil functioning, distributional changes of key species, linked to climate change, could significantly affect Antarctic soil functioning. We evaluated how the identity of six Antarctic plant, lichen and moss species relate to a range of soil attributes (C, N and P cycling), microbial abundance and structure in Livingston Island, Maritime Antarctica. We used an effect size metric to predict the association between species (vs. bare soil) and the measured soil attributes. We observed species-specific effects of the plant and biocrust species on soil attributes and microbial abundance. Phenols, phosphatase and β-D-cellobiosidase activities were the most important attributes characterizing the observed patterns. We found that the evaluated species positively correlated with soil nutrient availability and microbial abundance vs. bare soil. We provide evidence, from a comparative study, that plant and biocrust identity is associated with different levels of soil functioning and microbial abundance in Maritime Antarctica. Our results suggest that changes in the spatial distribution of these species linked to climate change could potentially entail changes in the functioning of Antarctic terrestrial ecosystems.

Effects of climate legacies on above- and belowground community assembly.

Abstract: The role of climatic legacies in regulating community assembly of above- and belowground species in terrestrial ecosystems remains largely unexplored and poorly understood. Here, we report on two separate regional and continental empirical studies, including >500 locations, aiming to identify the relative importance of climatic legacies (climatic anomaly over the last 20,000 years) compared to current climates in predicting the relative abundance of ecological clusters formed by species strongly co-occurring within two independent above- and belowground networks. Climatic legacies explained a significant portion of the variation in the current community assembly of terrestrial ecosystems (up to 15.4%) that could not be accounted for by current climate, soil properties, and management. Changes in the relative abundance of ecological clusters linked to climatic legacies (e.g., past temperature) showed the potential to indirectly alter other clusters, suggesting cascading effects. Our work illustrates the role of climatic legacies in regulating ecosystem community assembly and provides further insights into possible winner and loser community assemblies under global change scenarios.

Environmental drivers of the geographical distribution of methanotrophs: Insights from a national survey

Abstract: There is considerable evidence that environmental properties are important for microbial niche partitioning in general However, little is known about the environmental factors explaining this for soil methane-oxidising bacteria (or methanotrophs), which play an essential role in ecosystem functioning and climate regulation through mitigation of net CH4 emissions worldwide This knowledge gap limits the inclusion of taxon-based information to improve predictions of climate change-simulation models In this study, 697 soil samples were collected across Scotland and 62 climo-edaphic properties were analysed Combined with a set of hybrid geostatistical modelling approaches, the aim of this study was to investigate the biogeographical distribution (pmoA gene relative abundance) of key methanotrophic operational taxonomic units named Terminal-Restriction Fragments (T-RFs) and of methanotrophic community structure The main objectives were to: 1) identify major environmental drivers influencing the distribution and composition of methanotrophs; and 2) perform spatial modelling and mapping of soil methanotrophic community assemblage and distribution of those dominant T-RFs Herein, it was hypothesised that the assemblage of methanotrophic community and distribution of key populations across various landscapes could be predicted using a range of climo-edaphic factors optimised for spatial, climate and terrain attributes The findings presented here suggest that the distribution of methanotrophs is strongly linked to land use and some edaphic properties, predominantly soil moisture/rainfall, nutrients and metal ions The hybrid geostatistical approach allowed for spatial prediction of methanotrophic T-RFs and community, and demonstrated a clear niche partitioning between dominant T-RFs Overall, these results provide novel evidence that the distribution of methanotrophs could be explained and mapped in terms of niche partitioning and predicted at the regional scale The findings of the present study have significance for the sustainable management of ecosystems and improvement of simulation models for better prediction of ecosystem functions under predicted global changes

Ecological analyses of mycobacteria in showerhead biofilms and their relevance to human health

Abstract: Bacteria within the genus Mycobacterium can be abundant in showerheads, and the inhalation of aerosolized mycobacteria while showering has been implicated as a mode of transmission in nontuberculous mycobacterial (NTM) lung infections. Despite their importance, the diversity, distributions, and environmental predictors of showerhead-associated mycobacteria remain largely unresolved. To address these knowledge gaps, we worked with citizen scientists to collect showerhead biofilm samples and associated water chemistry data from 656 households located across the U.S. and Europe. Our cultivation-independent analyses revealed that the genus Mycobacterium was consistently the most abundant genus of bacteria detected in residential showerheads, yet mycobacterial diversity and abundances were highly variable. Mycobacteria were far more abundant, on average, in showerheads receiving municipal versus well water, and in U.S. households as compared to European households, patterns that are likely driven by differences in the use of chlorine disinfectants. Moreover, we found that water source, water chemistry, and household location also influenced the prevalence of specific mycobacterial lineages detected in showerheads. We identified geographic regions within the U.S. where showerheads have particularly high abundances of potentially pathogenic lineages of mycobacteria and these hot spots generally overlapped with those regions where NTM lung disease is most prevalent. Together these results emphasize the public health relevance of mycobacteria in showerhead biofilms. They further demonstrate that mycobacterial distributions in showerhead biofilms are often predictable from household location and water chemistry, knowledge that advances our understanding of NTM transmission dynamics and the development of strategies to reduce exposures to these emerging pathogens.

Microbial Modulators and Mechanisms of Soil Carbon Storage

Abstract: This chapter aims to provide a mechanistic understanding of the role microbes play in soil carbon (C) storage and propose pathways to include this data to modify existing ecological models. We found that the structure and function of soil microbial communities are controlled by complex interactions of biotic and abiotic site factors, while structural variations in soil microbial communities modulate transformation and/or turnover of soil C. We also demonstrated that inclusion of different microbial groups provides better predictions for different enzymatic activities involved in C degradation. Soil bacteria differ in their survival strategies and ability to influence the terrestrial C pool. We found that the effects of soil management practices of soil C turnover are modulated by the soil aggregate sizes and their associated microbial communities. The control of soil microbial communities on soil C turnover is much more pronounced in smaller sized aggregates. Altogether we demonstrate that soil microbial communities modulate soil C turnover from regional to global scale. Based on our findings, we propose that incorporation of microbial taxonomical and functional information in Earth ecosystem models will reduce uncertainty in model structure as these will represent temporal stability and adaptive responses of microbial communities and their interactions with the environment, which are critical considerations as we face environmental variations and rates of change.

Experimentally testing the species-habitat size relationship on soil bacteria: A proof of concept

Abstract: The species-area relationship is one of the most widely reported ecological theories accounting for biodiversity of plants and animals. However, we lack solid experimental data demonstrating whether this key ecological theorem also applies in the microbial world. Here, we conducted a microcosm study to evaluate the role of habitat area in driving the diversity, abundance, composition and functioning (i.e., four enzyme activities linked to organic matter decomposition) of soil bacterial communities. Thus, we aim to evaluate whether the principle of species-area relationship is potentially applicable to soil microbes. We established a fully factorial experimental design of three island sizes (∼9, 50 and 150 cm2) by two sterile soils (low, high resources). After six months of glasshouse incubation, habitat-area was positively related to bacterial richness, relative abundance of Chloroflexi, Verrucomicrobia and δ-proteobacteria, and soil functions in both soils. Soil with higher resources always had the greatest bacterial richness and functions. Our findings provide a proof of concept by demonstrating the potential importance of both habitat-area and resource availability in driving soil bacterial biodiversity and functioning.

Intraspecies variation in a widely distributed tree species regulates the responses of soil microbiome to different temperature regimes.

Abstract: Plant characteristics in different provenances within a single species may vary in response to climate change, which might alter soil microbial communities and ecosystem functions. We conducted a glasshouse experiment and grew seedlings of three provenances (temperate, subtropical and tropical origins) of a tree species (i.e., Eucalyptus tereticornis) at different growth temperatures (18, 21.5, 25, 28.5, 32 and 35.5°C) for 54 days. At the end of the experiment, bacterial and fungal community composition, diversity and abundance were characterized. Measured soil functions included surrogates of microbial respiration, enzyme activities and nutrient cycling. Using Permutation multivariate analysis of variance (PerMANOVA) and network analysis, we found that the identity of tree provenances regulated both structure and function of soil microbiomes. In some cases, tree provenances substantially affected the response of microbial communities to the temperature treatments. For example, we found significant interactions of temperature and tree provenance on bacterial community and relative abundances of Chloroflexi and Zygomycota, and inorganic nitrogen. Microbial abundance was altered in response to increasing temperature, but was not affected by tree provenances. Our study provides novel evidence that even a small variation in biotic components (i.e., intraspecies tree variation) can significantly influence the response of soil microbial community composition and specific soil functions to global warming.

Unraveling the effects of spatial variability and relic DNA on the temporal dynamics of soil microbial communities

Abstract: Few studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that the belowground environment is dynamic. In part, this stems from the challenges associated with the high degree of spatial heterogeneity in soil microbial communities and because the presence of relic DNA (DNA from non-living cells) may dampen temporal signals. Here we disentangle the relationships among spatial, temporal, and relic DNA effects on bacterial, archaeal, and fungal communities in soils collected from contrasting hillslopes in Colorado, USA. We intensively sampled plots on each hillslope over six months to discriminate between temporal variability, intra-plot spatial heterogeneity, and relic DNA effects on the soil prokaryotic and fungal communities. We show that the intra-plot spatial variability in microbial community composition was strong and independent of relic DNA effects with these spatial patterns persisting throughout the study. When controlling for intra-plot spatial variability, we identified significant temporal variability in both plots over the six-month study. These microbial communities were more dissimilar over time after relic DNA was removed, suggesting that relic DNA hinders the detection of important temporal dynamics in belowground microbial communities. We identified microbial taxa that exhibited shared temporal responses and show these responses were often predictable from temporal changes in soil conditions. Our findings highlight approaches that can be used to better characterize temporal shifts in soil microbial communities, information that is critical for predicting the environmental preferences of individual soil microbial taxa and identifying linkages between soil microbial community composition and belowground processes. Importance Nearly all microbial communities are dynamic in time. Understanding how temporal dynamics in microbial community structure affect soil biogeochemistry and fertility are key to being able to predict the responses of the soil microbiome to environmental perturbations. Here we explain the effects of soil spatial structure and relic DNA on the determination of microbial community fluctuations over time. We found that intensive spatial sampling is required to identify temporal effects in microbial communities because of the high degree of spatial heterogeneity in soil and that DNA from non-living microbial cells masks important temporal patterns. We identified groups of microbes that display correlated behavior over time and show that these patterns are predictable from soil characteristics. These results provide insight into the environmental preferences and temporal relationships between individual microbial taxa and highlight the importance of considering relic DNA when trying to detect temporal dynamics in belowground communities.

Soil Nutrients and Soil Carbon Storage : Modulators and Mechanisms

Abstract: It is well recognized that the capacity of soils to sequester carbon (C) is strongly influenced by nitrogen (N) and phosphorus (P) availability because of the strong stoichiometric links between these biogeochemical cycles. Human disturbance (e.g., deposition, fertilization, and mining), has, and continue to have, caused large imbalances between the biogeochemical cycles and changing nutrient availabilities identified as a key uncertainty in predicting future ecosystem C sequestration. Despite this knowledge, key gaps exist in our understanding of the mechanisms that drive the interactions between C and nutrient cycles, which limit our ability to predict the impacts of change on future soil C sequestration. In this chapter, we discuss N, P, and other nutrients as key modulators of soil C storage. We consider two contrasting mechanistic theories—microbial nutrient mining (MNM) theory and basic stoichiometric decomposition theory—driving these modulators, as well as the impact that environment and land-use change is likely to have, and the expected consequences for soil C storage. Overwhelmingly, experimental evidence from the micro- to global-scale support MNM theory as the main mechanism of the impact of nutrients on soil C storage, and suggest that increasing N availability inhibits enzymes responsible for recalcitrant C degradation and thus promotes long-term C storage in soils. A better mechanistic understanding of the interactions between resource and biomass stoichiometry, microbial nutrient use efficiency, and litter chemistry, as well as improved knowledge of P mineralization, sorption, limitation, and stoichiometry is needed to improve parameterization of N- and P cycling into C-cycling models.